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Overview

  • Task: Segment aorta on CT. This method can produce high-accuracy results - the more user inputs are provided, the more accurate the results will be. The same method can be used for segmenting other structures that have a good contrast compared to the background but there are other structures with similar intensity nearby.
  • Imaging modality: any.

Prerequisites

  • SegmentEditorExtraEffects extension is installed.
  • Slicer-4.10 or later.

Recommended workflow

  • Create a segment for aorta and use Paint effect to paint a few strokes inside the aorta.
  • Select Threshold effect, set slider to highlight the aorta, and click Use for masking.
  • Create a segment for all other structures and paint in regions that have similar intensity as the aorta but it is not the aorta (bones, other vessels, etc.).
  • Select Grom from seeds effect and click Initialize to compute segmentation preview.
  • Inspect segmentation. If any region is misclassified then paint more strokes using the aorta or the other segment.
  • Click Apply when segmentation preview is satisfactory to finalize the segmentation.
  • Apply Smoothing effect, Median method to fill in missed voxels and smooth outer surface of the vessel.

Tips:

  • To make paint strokes more visible, you can deactivate Paint effect and left-click-and-drag in the slice view to change background volume window/level.
  • To see preview in 3D view: Click the down-arrow button on the right side of Show 3D button and disable Surface smoothing (this will make updates of 3D visualization very fast). Click Show 3D button.
  • If a the segmentation does not extend to the entire aorta then paint strokes in the missing parts and reinitialize (click Cancel and then click Initialize).
  • To quickly activate/deactivate Paint effect hit 1 key.
  • To quickly switch between segments, effect hit q or w key.

Example

  • Download CTACardio sample data set
  • Go to Segment editor module, click Add button to create a new segment
  • Select Threshold effect, set slider to highlight the aorta, and click Use for masking.

Thresholding defines intensity range for aorta.

  • Double-click Color column to show segment terminology/color selector, typ aorta, then hit Enter (or click Select)

Define standard terminology and color for aorta segment.

  • Select Paint effect and paint a few strokes inside the aorta using aorta segment, and paint outside the aorta using the other segment. Regions painted with aorta segment will be included, regions painted with the other segment will be excluded from the final aorta segmentation.

Paint seeds inside and outside the aorta using aorta and other segment.

  • Click Initialize to compute segmentation preview.

Segmentation preview is shown after clicking Initialize.

  • If a non-aorta region (e.g., ribs, heart, or other vessels) are shown in the preview as part of the aorta, then paint it over using the other segment. If part of aorta region is missed in the preview as part of the aorta, paint it over using the aorta segment.

Heart ventricles and atria excluded by painting a stroke with the other segment.

  • To see preview in 3D view: Click Show 3D button next to the Display inputs/outputs slider.

Preview segmentation result in 3D.

  • Paint strokes using aorta and other segment as needed. Click Apply when segmentation preview is satisfactory.

Segmentation finalized.

  • Apply Smoothing effect, Median method to fill in missed voxels and smooth outer surface of the vessel.

Final result.

Final result:

Animation of final result.